1HYT

RE-DETERMINATION AND REFINEMENT OF THE COMPLEX OF BENZYLSUCCINIC ACID WITH THERMOLYSIN AND ITS RELATION TO THE COMPLEX WITH CARBOXYPEPTIDASE A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Redetermination and refinement of the complex of benzylsuccinic acid with thermolysin and its relation to the complex with carboxypeptidase A.

Hausrath, A.C.Matthews, B.W.

(1994) J.Biol.Chem. 269: 18839-18842


  • PubMed Abstract: 
  • The complex of benzylsuccinic acid with thermolysin has been redetermined at 1.7-A resolution and refined to a crystallographic residual of 15.7%. In contrast to the prior study, which was to 2.3-A resolution, and without the benefit of refinement (B ...

    The complex of benzylsuccinic acid with thermolysin has been redetermined at 1.7-A resolution and refined to a crystallographic residual of 15.7%. In contrast to the prior study, which was to 2.3-A resolution, and without the benefit of refinement (Bolognesi, M. C. and Matthews, B. W. (1979) J. Biol. Chem. 254, 634-639), the present analysis shows that it is the D- rather than the L-isomer of benzylsuccinic acid that binds. The stereochemistry of the zinc-carboxylate interaction is now seen to be syn, as is also observed in all known zinc-carboxylate complexes of both thermolysin and carboxypeptidase A. The mode of binding of the beta-carboxylate resembles the presumed geometry of the tetrahedral transition state and, as such, is consistent with the commonly accepted mechanism of action of thermolysin and of carboxypeptidase A.


    Related Citations: 
    • Structure of Thermolysin Refined at 1.6 Angstroms Resolution
      Holmes, M.A.,Matthews, B.W.
      (1982) J.Mol.Biol. 160: 623
    • Binding of N-Carboxymethyl Dipeptide Inhibitors to Thermolysin Determined by X-Ray Crystallography: A Novel Class of Transition-State Analogues for Zinc Peptidases
      Monzingo, A.F.,Matthews, B.W.
      (1984) Biochemistry 23: 5724
    • The Conformation of Thermolysin
      Matthews, B.W.,Weaver, L.H.,Kester, W.R.
      (1974) J.Biol.Chem. 249: 8030
    • Structure of Thermolysin
      Matthews, B.W.,Colman, P.M.,Jansonius, J.N.,Titani, K.,Walsh, K.A.,Neurath, H.
      (1972) Nature New Biol. 238: 41
    • Three Dimensional Structure of Thermolysin
      Matthews, B.W.,Jansonius, J.N.,Colman, P.M.,Schoenborn, B.P.,Duporque, D.
      (1972) Nature New Biol. 238: 37


    Organizational Affiliation

    Institute of Molecular Biology, University of Oregon, Eugene 97403.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
THERMOLYSIN
A
316Bacillus thermoproteolyticusGene Names: npr
EC: 3.4.24.27
Find proteins for P00800 (Bacillus thermoproteolyticus)
Go to UniProtKB:  P00800
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
BZS
Query on BZS

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Download CCD File 
A
L-BENZYLSUCCINIC ACID
C11 H12 O4
GTOFKXZQQDSVFH-SECBINFHSA-N
 Ligand Interaction
DMS
Query on DMS

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Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 93.691α = 90.00
b = 93.691β = 90.00
c = 131.503γ = 120.00
Software Package:
Software NamePurpose
TNTrefinement
NIELSENdata reduction
XUONG)data reduction
XENGENdata reduction
XUONG)data scaling
XENGENdata scaling
NIELSENdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-07-31
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2012-06-13
    Type: Derived calculations
  • Version 1.4: 2017-11-29
    Type: Derived calculations, Other